By default, secure storage is located in your home directory. On Windows that typically resolves to "C:\Documents and Settings\<user_name>\.eclipse\org.eclipse.equinox.security". This location is selected to allow multiple Eclipse-based applications to share the same secure storage.
If you would like to modify the location of the default secure storage, you can use the "-eclipse.keyring <file_path>" runtime option. The <file_path> is a path to the file which is used to persist the secure storage data.
The current location of the default secure storage can be found on the General > Security > Secure Storage preferences page.
The password provider mechanism can be bypassed if you specify the "-eclipse.password <file path>" runtime option. In this case the contents of the file you specified as the argument will be used as a master password. While this option is valuable in some circumstances (such as headless applications), the protection of the password file becomes a consideration. The password file can be protected by the operating system access rights and/or by placing it on a removable storage, such as a USB key.
How secure storage works
Life of a master password
Secure storage preference page